Many important enzymes in prokaryotes and eukaryotes are subject to covalent modification mediated by mixed-function oxidation systems. The modified enzymes are frequently rendered catalytically inactive. In the case of bacterial glutamine synthetase, the covalent modification "marks" the protein for subsequent proteolytic degradation by a protease which recognizes the modified protein. A peptide from the modified protein has lost a single histidine residue. Its sequence (MET-HIS*-CYS-HIS-MET) shows it to be rich in chelating residues. This peptide could bind the metal cation required for mixed-function oxidation, thus explaining the site-specific free radical reaction. However, the modifed histidine is not the only residue altered upon oxidation. A carbonyl moiety is introduced into a residue located in a different peptide. This carbonyl moiety has been detected in several modified enzymes whose histidine content was unchanged. The oxidative modification functions physiologically to rapidly inactivate the glycerol dehydrogenase of Klebsiella aerogenes upon shift from an anaerobic to aerobi environment. This inactivation may prevent the accumulation of toxic products which could be produced by the enzyme in an aerobic environment. The covalent modification produced by mixed-function oxidation was also detected in phosphoglycerate kinase purified from aged rats. Mixed-function oxidation may explain the altered properties noted in many enzymes during aging.